Phylogenetics
The two components of the genome have very distinct molecular evolutionary histories and likely to be under very different evolutionary pressures. The DNA B genome originated as a satellite that was captured by the monopartite progenitor of all extant bipartite begomoviruses and has subsequently evolved to become an essential genome component.
More than 133 begomovirus species having monopartite genomes are known: all originate from the Old World. No monopartite begomoviruses native to the New World have yet been identified.
Phylogenetic analysis is based on the A component. B components may be exchanged between species and may result in new species.
Analysis of the genus reveals a number of clades. The main division is between the Old and New World strains. The Old World strains can be divided into African, Indian, Japanese and other Asian clades with a small number of strains grouping outside these. The New World strains divide into Central and Southern America strains.
Along with these main groupings are a number of smaller clades. One group infecting a range of legumes originating from India and Southeast Asia (informally 'Legumovirus') and a set of viruses isolated from Ipomoea species originating from America, Asia and Europe (informally 'Sweepovirus') appear to be basal to all the other species. Two species isolated from Corchorus from Vietnam (informally 'Corchovirus') somewhat unexpectedly group with the New World species.
Read more about this topic: Begomovirus